In silico identification of conserved microRNAs in large number of diverse plant species

BackgroundMicroRNAs (miRNAs) are recently discovered small non-coding RNAs that play pivotal roles in gene expression, specifically at the post-transcriptional level in plants and animals. Identification of miRNAs in large number of diverse plant species is important to understand the evolution of miRNAs and miRNA-targeted gene regulations. Now-a-days, publicly available databases play a central role in the in-silico biology. Because, at least ~21 miRNA families are conserved in higher plants, a homology based search using these databases can help identify orthologs or paralogs in plants.ResultsWe searched all publicly available nucleotide databases of genome survey sequences (GSS), high-throughput genomics sequences (HTGS), expressed sequenced tags (ESTs) and nonredundant (NR) nucleotides and identified 682 miRNAs in 155 diverse plant species. We found more than 15 conserved miRNA families in 11 plant species, 10 to14 families in 10 plant species and 5 to 9 families in 29 plant species. Nineteen conserved miRNA families were identified in important model legumes such as Medicago, Lotus and soybean. Five miRNA families – miR319, miR156/157, miR169, miR165/166 and miR394 – were found in 51, 45, 41, 40 and 40 diverse plant species, respectively. miR403 homologs were found in 16 dicots, whereas miR437 and miR444 homologs, as well as the miR396d/e variant of the miR396 family, were found only in monocots, thus providing large-scale authenticity for the dicot- and monocot-specific miRNAs. Furthermore, we provide computational and/or experimental evidence for the conservation of 6 newly found Arabidopsis miRNA homologs (miR158, miR391, miR824, miR825, miR827 and miR840) and 2 small RNAs (small-85 and small-87) in Brassica spp.ConclusionUsing all publicly available nucleotide databases, 682 miRNAs were identified in 155 diverse plant species. By combining the expression analysis with the computational approach, we found that 6 miRNAs and 2 small RNAs that have been identified only in Arabidopsis thus far, are also conserved in Brassica spp. These findings will be useful for tracing the evolution of small RNAs by examining their expression in common ancestors of the Arabidopsis-Brassica lineage.

[1]  Hai Huang,et al.  SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. , 2006, The Plant journal : for cell and molecular biology.

[2]  R. Sunkar,et al.  Posttranscriptional Induction of Two Cu/Zn Superoxide Dismutase Genes in Arabidopsis Is Mediated by Downregulation of miR398 and Important for Oxidative Stress Tolerance[W] , 2006, The Plant Cell Online.

[3]  C. Helliwell,et al.  Molecular evolution and selection of a gene encoding two tandem microRNAs in rice , 2007, FEBS letters.

[4]  Baohong Zhang,et al.  Identification of 188 conserved maize microRNAs and their targets , 2006, FEBS letters.

[5]  D. Bartel,et al.  Common Functions for Diverse Small RNAs of Land Plants[W][OA] , 2007, The Plant Cell Online.

[6]  S. Cox,et al.  Evidence that miRNAs are different from other RNAs , 2006, Cellular and Molecular Life Sciences CMLS.

[7]  D. Bartel,et al.  A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. , 2006, Genes & development.

[8]  Vincent L. Chiang,et al.  Novel and Mechanical Stress–Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsisw⃞ , 2005, The Plant Cell Online.

[9]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[10]  T. Shikanai,et al.  Regulation of Copper Homeostasis by Micro-RNA in Arabidopsis* , 2007, Journal of Biological Chemistry.

[11]  Gang Wu,et al.  Nuclear processing and export of microRNAs in Arabidopsis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Gi-Ho Sung,et al.  Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana , 2004, Nature Genetics.

[13]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

[14]  Yuichiro Watanabe,et al.  Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  N. Fedoroff,et al.  The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Vrebalov,et al.  Self-Incompatibility in the Genus Arabidopsis: Characterization of the S Locus in the Outcrossing A. lyrata and Its Autogamous Relative A. thaliana , 2001, Plant Cell.

[17]  P. Rouzé,et al.  Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Thomas Girke,et al.  Cloning and Characterization of MicroRNAs from Ricew⃞ , 2005, The Plant Cell Online.

[19]  Michael B. Stadler,et al.  MicroRNA-Mediated Regulation of Stomatal Development in Arabidopsis[W][OA] , 2007, The Plant Cell Online.

[20]  J. Cavaille,et al.  A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. , 2004, Genome research.

[21]  Peter F Stadler,et al.  Molecular evolution of a microRNA cluster. , 2004, Journal of molecular biology.

[22]  Shivakundan Singh Tej,et al.  MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. , 2006, Genome research.

[23]  Hajime Sakai,et al.  Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016238. , 2003, The Plant Cell Online.

[24]  Cathie Martin,et al.  SERRATE: a new player on the plant microRNA scene , 2006, EMBO reports.

[25]  D. Bartel,et al.  Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. , 2005, RNA.

[26]  Wen-Hsiung Li,et al.  Rates of Nucleotide Substitution in Angiosperm Mitochondrial DNA Sequences and Dates of Divergence Between Brassica and Other Angiosperm Lineages , 1999, Journal of Molecular Evolution.

[27]  Xuemei Chen,et al.  Methylation as a Crucial Step in Plant microRNA Biogenesis , 2005, Science.

[28]  Thomas Girke,et al.  Identification and characterization of endogenous small interfering RNAs from rice , 2005, Nucleic acids research.

[29]  L. Mao,et al.  Molecular evolution of the rice miR395 gene family , 2005, Cell Research.

[30]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[31]  Ramanjulu Sunkar,et al.  Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. , 2007, Trends in plant science.

[32]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[33]  D. Bartel,et al.  Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. , 2004, Molecular cell.

[34]  Z. Yang,et al.  Computational identification of novel microRNAs and targets in Brassica napus , 2007, FEBS letters.

[35]  Jason S. Cumbie,et al.  High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes , 2007, PloS one.

[36]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[37]  Jonathan D. G. Jones,et al.  A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling , 2006, Science.

[38]  Adam M. Gustafson,et al.  microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants , 2005, Cell.

[39]  B. Meyers,et al.  An expression atlas of rice mRNAs and small RNAs , 2007, Nature Biotechnology.

[40]  M. Stitt,et al.  PHO2, MicroRNA399, and PHR1 Define a Phosphate-Signaling Pathway in Plants1[W][OA] , 2006, Plant Physiology.

[41]  R. Sunkar,et al.  Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis , 2004, The Plant Cell Online.

[42]  H. Vaucheret,et al.  Functions of microRNAs and related small RNAs in plants , 2006, Nature Genetics.

[43]  W. Frank,et al.  Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss. , 2006, The Plant journal : for cell and molecular biology.

[44]  Chun-Lin Su,et al.  Regulation of Phosphate Homeostasis by MicroRNA in Arabidopsis[W] , 2005, The Plant Cell Online.

[45]  Jian-Kang Zhu,et al.  A miRNA Involved in Phosphate-Starvation Response in Arabidopsis , 2005, Current Biology.

[46]  Shivakundan Singh Tej,et al.  Elucidation of the Small RNA Component of the Transcriptome , 2005, Science.

[47]  Baohong Zhang,et al.  Conservation and divergence of plant microRNA genes. , 2006, The Plant journal : for cell and molecular biology.

[48]  Fang Liu,et al.  Identification of cotton microRNAs and their targets. , 2007, Gene.

[49]  Chun-Lin Su,et al.  pho2, a Phosphate Overaccumulator, Is Caused by a Nonsense Mutation in a MicroRNA399 Target Gene1[W] , 2006, Plant Physiology.

[50]  Guillaume Blanc,et al.  Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes , 2004, The Plant Cell Online.

[51]  Baohong Zhang,et al.  Identification and characterization of new plant microRNAs using EST analysis , 2005, Cell Research.

[52]  David P. Bartel,et al.  A Two-Hit Trigger for siRNA Biogenesis in Plants , 2006, Cell.

[53]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[54]  Hanah Margalit,et al.  Clustering and conservation patterns of human microRNAs , 2005, Nucleic acids research.

[55]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[56]  Xuemei Chen,et al.  A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development , 2004, Science.

[57]  Yun Zheng,et al.  Identification of novel and candidate miRNAs in rice by high throughput sequencing , 2008, BMC Plant Biology.

[58]  Sarah Hake,et al.  The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA , 2007, Nature Genetics.